R'MES: Formating Results

The rmes.format program displays the results contained in an output file generated by the rmes command. It produces a table with the motifs sorted according to their exceptionality scores (quantities such like observed counts, expected counts, scores etc. are also presented).

It has to be run via a command line which looks like :

rmes.format [options] < <rmesfilename> > <tablefilename>

where

<rmesfilename>
indicates the filename of the output file generated by the rmes command,
<tablefilename>
specifies the name of the output file.

All the options can be obtained by typing :

rmes.format --help

and are described below:

-l <int> or --length <int>
(value required) sets the length of the analyzed words,
-i <int> or --lmin <int>
(value required) sets the length of the smallest analyzed words,
-a <int> or --lmax <int>
(value required) sets the length of the largest analyzed words,
--tmax <float value>
(value required) motifs with a score greater or equal to this threshold will be displayed (3 by default),
--tmin <float value>
(value required) motifs with a score less or equal to this threshold will be displayed (-3 by default),
-v or --version
displays version information and exits.

For more details, please refer to the user guide

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Article | by Dr. Radut